[gmx-users] Modeling Zinc in OPLS

[Anton Feenstra]

Sandeep Somani wrote:

> Hi Maik
> 
> In my protein the Zn is bonded to 3 CYS and a HIS and is stabilising the
> local structure. 
> 
> So ill also have to use the bonded approach which means there will be
> change in parameters for the surrounding CYS and HIS too (?). 

A few comments:

- I know of some people who did a lot of optimization of ff paramters 
for Zn in azurin (a Zn containing enzyme), and finally concluded that 
you *do* indeed need the bonded approach. (This may ofcourse be 
different for other proteins.)

- Try to think of this as modelling the interaction potential that you 
may expect between Zn and its coordination partners, and not in terms of 
(non-)covalent bonding. Would the potential barrier be high enough to 
prevent breaking at room temperature (that is, is it higher than, say, 4 
or 5*kT?)? If so, it makes sense to model it 'bonded'. Another angle to 
look at it, is whould you *want* the coordination to be able to break 
and/or change? If not, make it bonded.

- Finally, for the parameters of the coordination partners (CYS/HIS), 
changing these may not be (entirely) necessary. You may expect changes 
in charge distribution, and, logically, in bond lengts, angles and 
oscillator strengths (force constant) as well, but these may not be 
critical to your purposes.


-- 
Groetjes,

Anton

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|  _   _  ___,| K. Anton Feenstra                                     |
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